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PDBsum entry 1vfn
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Nucleoside phosphorylase
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PDB id
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1vfn
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References listed in PDB file
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Key reference
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Title
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Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 a resolution.
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Authors
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G.Koellner,
M.Luić,
D.Shugar,
W.Saenger,
A.Bzowska.
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Ref.
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J Mol Biol, 1997,
265,
202-216.
[DOI no: ]
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PubMed id
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Abstract
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Trimeric calf spleen purine nucleoside phosphorylase has been complexed with
hypoxanthine via phosphorolysis of inosine in the presence of phosphate. The
resulting, "Michaelis" complex (three hypoxanthine molecules per trimer),
presumed to be formed under these conditions, crystallized in the cubic space
group P2(1)3, with unit cell dimension a = 94.11 A and one monomer in the
asymmetric crystal unit; the biologically active trimer is located on the
crystallographic 3-fold axis. High-resolution X-ray diffraction data were
collected using synchrotron radiation (EMBL outstation, Hamburg, c/o DESY). The
crystal structure has been determined by molecular replacement and refined at
2.15 A resolution to an R-value of 0.18. In the hypoxanthine binding site, a
cis-peptide bond between Asn243 and Lys244 is observed. Side-chains of GIu201
and Asn243, as well as one integral water molecule located in the base binding
site, form hydrogen bonds with the hypoxanthine N-1 H, N-7 H and O-6. A second
water molecule links the base positions N-3 and N-9 with an adjacent pocket,
which presumably is the phosphate-binding site. This pocket is filled completely
by a cluster of six water molecules. Hence all possible donor/acceptor-positions
of hypoxanthine are saturated by hydrogen-bonding to protein side-chains or
integral water molecules. Purine nucleoside phosphorylase isolated form human
tissues is a primary target for chemotherapeutic intervention, and the more
stable calf enzyme has similar physico-chemical and kinetic properties, as well
as response to inhibitors. Hence the high-resolution structure presented here
may serve for design of inhibitors with potential pharmacological applications.
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Figure 4.
Figure 4. Mode of binding of the unidentified metal cation
(see the text and Figure 1) located on the 3-fold axis. The
cation is coordinated by His20 N^  epsilon
of three symmetry-related trimers and water molecules Wat429 and
Wat430. Hydrogen bond lengths are denoted in Å (drawn with
SCHAKAL; [Keller 1988]).
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Figure 5.
Figure 5. A drawing of the trimeric calf spleen PNP-Hx
complex. The location of the unidentified metal cation (see also
Figure 2 and Figure 4) is shown as a circle with enlarged van
der Waals radius in each monomer. Direct contacts between
monomers forming the trimer are mainly from the loop between
residues 141 and 168 of one monomer, which is the longest loop
belting the monomer from one side (in red, see also (Table 4 and
Table 4)). Drawn with MOLSCRIPT [Kraulis 1991].
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1997,
265,
202-216)
copyright 1997.
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Secondary reference #1
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Title
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Calf spleen purine nucleoside phosphorylase: purification, Sequence and crystal structure of its complex with an n(7)-Acycloguanosine inhibitor.
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Authors
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A.Bzowska,
M.Luić,
W.Schröder,
D.Shugar,
W.Saenger,
G.Koellner.
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Ref.
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Febs Lett, 1995,
367,
214-218.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. (A) Chemical structure of 7-[(1,3-dihydroxypropyl-
2)amino]ethylguanine. (B) Omit difference electron density superim-
with the 7-[(1,3-dihydroxypropyl-2)amino]ethylguanine model
([IFol-lFcl[ map at 2xrms). Inhibitor model atoms were
ot included in the structure factor calculation.
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Figure 3.
ig. 3. Mode of binding of 7-[(1,3-dihydroxy-propyl-2)amino]
ethylguanine in the ctive site of calf spleen PNP (white). Possible
hydrogen bond lengths an angles (hydrogen Donor
... Acceptor were calculated where possible) are:
Inhibitor Ol7-Ser 22° O~ 2.65/~; Inhibitor O17-Arg 84 Ne 2.79 ~ (106°);
OlS-Ala jl6 2.66/~ (138°); Inhibitor OtS-Ala H60 3.10 ~;
nhibitor NJ2-AIa 't60 3.11 A (152°); Inhibitor N'2-Ser 2° 2 / 3.33/k
(151°); Inhibitor N7-Water A 3.41 /~; Inhibitor N9-Water B 3.00 ./k;
B-Glu 259 O 2.32/~; Inhibitor N2As 243 05 2.41 A. For compar-
of binding of guanine in the active site of human erythrocyte
is givn (black, n italic) [14]. The figure drawn with
SCHAKAL 88 [39].
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The above figures are
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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